Proteomics is the study of the structure and function of proteins in biological systems. It has a wide range of applications starting from protein expression profiling in healthy versus diseased states of an organism to analyzing the interaction of proteins in living organisms to mapping of protein modifications and identification of how, when, and where proteins are modified within a living cell. We are developing an approach for the large-scale, massively parallel digital counting of proteins and peptide sequencing based on single molecule detection and a microfluidic platform technology. This revolutionary protein measurement platform will significantly reduce the amount of sample required for analysis and allow identification of low abundance proteins without bias. This innovation will have far-reaching impacts on quantitative systems biology, disease biomarker discovery and validation, clinical diagnostics, and personalized medicine. Pharmaceutical-, reagent supply- and instrumentation companies have paid substantial premiums to acquire technologies that promise to more quickly and efficiently identify targets for both therapeutics and diagnostics. We expect successful release of the proposed instrument will generate substantial revenue in an already growing marketplace.